Contacts of the helix formed by residues 214 - 226 (chain A) in PDB entry 4DHZ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 214 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A TYR* 4.0 20.0 + - - +
212A ASP 4.1 1.8 + - - -
213A ALA* 1.3 72.4 - - - +
215A HIS* 1.3 67.9 + - - +
216A LEU* 3.3 4.0 - - + +
217A ALA* 3.0 8.1 + - - +
218A ILE* 2.8 34.0 + - - +
542B ARG* 3.4 24.7 + - - -
570B VAL* 6.2 1.1 - - - -
571B LEU 3.9 11.4 - - - +
572B ARG* 4.9 0.9 - - - -
573B LEU 3.9 0.5 + - - -
574B ARG* 3.4 42.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A ASP* 1.3 78.9 + - - +
216A LEU* 1.3 57.3 + - - +
218A ILE* 3.0 11.7 + - + +
219A ASN* 2.8 32.7 + - + +
248A ILE* 4.5 19.3 - - + +
508B LEU* 3.6 29.9 - - + +
509B THR* 5.7 7.7 - - + +
569B LEU* 5.2 1.8 - - + -
570B VAL* 3.6 12.7 - - + -
571B LEU* 2.7 65.2 + - + +
573B LEU* 3.8 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A LEU* 4.2 19.5 - - + -
188A TYR* 4.0 19.7 - - + +
191A PHE* 4.0 18.4 - - + +
192A ILE* 3.8 30.7 - - + +
201A TYR* 4.1 28.0 - - + +
214A ASP* 3.3 2.5 - - + +
215A HIS* 1.3 77.6 - - - +
217A ALA* 1.3 55.6 + - - +
219A ASN* 3.6 3.0 + - + +
220A SER* 2.7 32.6 + - - +
508B LEU* 3.9 31.3 - - + +
570B VAL* 5.4 6.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A PHE* 4.9 1.3 - - - -
90A TYR* 3.6 23.6 - - - +
177A THR* 3.4 13.4 - - + +
201A TYR* 4.8 5.1 + - - +
206A ILE* 3.9 22.0 - - + +
213A ALA* 4.4 4.9 - - + -
214A ASP* 3.0 19.0 + - - +
216A LEU* 1.3 75.0 - - - +
218A ILE* 1.3 67.2 + - - +
220A SER* 3.1 2.7 + - - -
221A LEU* 2.9 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A PHE* 3.6 42.2 - - + -
213A ALA* 4.4 4.5 - - + +
214A ASP* 2.8 23.0 + - - +
215A HIS* 3.3 8.3 - - + +
217A ALA* 1.3 77.2 - - - +
219A ASN* 1.3 65.1 + - - +
221A LEU 3.5 0.2 + - - -
222A ILE* 3.3 27.2 + - + +
231A ILE* 4.1 7.0 - - + -
248A ILE* 3.8 25.4 - - + -
268A TYR* 3.2 30.5 - - + +
573B LEU* 3.6 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A PHE* 5.1 0.3 - - - -
188A TYR* 3.5 19.8 + - - -
215A HIS* 2.8 22.9 + - + +
216A LEU* 3.8 5.4 - - + +
218A ILE* 1.3 77.2 - - - +
220A SER* 1.3 62.7 + - - +
222A ILE* 3.4 1.4 + - - +
223A LYS* 3.0 57.9 + - - +
248A ILE* 3.6 22.7 - - - +
508B LEU* 4.0 33.9 + - + +
509B THR* 5.5 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A THR* 3.8 22.4 - - - -
180A PHE* 3.7 27.9 - - - -
181A LEU* 3.4 21.0 - - - +
188A TYR* 5.4 1.7 - - - -
216A LEU* 2.7 22.2 + - - +
217A ALA* 3.1 6.5 + - - -
219A ASN* 1.3 78.9 + - - +
221A LEU* 1.3 54.0 + - - +
224A ALA* 2.7 38.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A PHE* 3.5 29.4 - - + -
90A TYR* 3.7 20.4 - - + +
93A ILE* 3.8 30.1 - - + -
173A PHE* 3.5 34.8 - - + +
176A ILE* 4.1 11.0 - - + -
177A THR* 3.3 25.3 - - + +
217A ALA 2.9 13.7 + - - +
218A ILE 4.1 0.2 - - - +
220A SER* 1.3 74.8 - - - +
222A ILE* 1.3 54.2 + - - +
224A ALA* 4.4 2.9 - - - -
225A ALA* 2.7 40.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A PHE* 4.4 6.7 - - + -
93A ILE* 4.4 11.7 - - + -
218A ILE* 3.3 36.9 + - + +
219A ASN 3.7 2.7 - - - +
221A LEU* 1.3 79.7 - - - +
223A LYS* 1.3 60.4 - - + +
225A ALA 3.5 0.2 + - - -
226A GLY* 3.1 20.8 + - - -
227A THR* 3.2 32.5 + - + +
228A ARG 4.8 0.2 - - - +
229A VAL* 4.0 29.4 - - + -
248A ILE* 3.4 50.3 - - + +
249A PRO* 4.4 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A PHE* 3.6 29.2 - - + -
188A TYR* 4.3 8.5 - - - +
219A ASN* 3.0 52.0 + - - +
220A SER 4.0 0.2 - - - +
222A ILE* 1.3 78.8 - - + +
224A ALA* 1.3 66.3 + - - +
226A GLY* 3.0 14.4 + - - -
227A THR 5.6 0.4 - - - -
248A ILE* 4.5 1.0 - - - +
249A PRO* 3.4 34.0 - - + +
508B LEU 4.5 8.8 + - - -
509B THR* 5.6 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A PHE* 5.7 0.2 - - - -
118A TRP* 3.6 34.1 + - + -
176A ILE* 4.0 19.3 - - + +
180A PHE* 3.6 31.7 - - + -
220A SER 2.7 22.9 + - - +
221A LEU* 3.8 3.6 - - - +
223A LYS* 1.3 73.9 - - - +
225A ALA* 1.3 60.1 + - - +
226A GLY* 3.5 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ILE* 5.3 0.4 - - + -
97A LEU* 4.1 22.1 - - + +
107A ARG* 5.2 1.4 + - - -
111A PHE* 3.6 27.1 - - + -
118A TRP* 5.7 0.2 - - - +
173A PHE* 5.4 0.4 - - + -
176A ILE* 4.3 12.1 - - + +
221A LEU* 2.7 27.0 + - + +
222A ILE 3.9 3.8 - - - +
223A LYS 3.2 0.2 - - - -
224A ALA* 1.3 73.6 - - - +
226A GLY* 1.3 63.2 + - - +
227A THR* 3.9 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ARG* 3.1 18.0 + - - -
222A ILE 3.1 1.9 + - - -
223A LYS* 3.0 15.7 + - - -
224A ALA 3.2 0.6 + - - -
225A ALA* 1.3 80.7 - - - +
227A THR* 1.3 60.6 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il